Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch
comparison 0.2.0/modules/custom/qual_passed_genomes/main.nf @ 0:9e8b1c747a6a draft default tip
planemo upload
| author | galaxytrakr |
|---|---|
| date | Fri, 29 May 2026 13:32:17 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:9e8b1c747a6a |
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| 1 process QUAL_PASSED_GENOMES { | |
| 2 tag "Consolidate" | |
| 3 label "process_micro" | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : | |
| 9 'quay.io/biocontainers/python:3.10.4' }" | |
| 10 | |
| 11 input: | |
| 12 path acc_passed_tool1 | |
| 13 path acc_passed_tool2 | |
| 14 | |
| 15 output: | |
| 16 path 'accs_passed.txt', emit: accs | |
| 17 path 'versions.yml' , emit: versions | |
| 18 | |
| 19 when: | |
| 20 task.ext.when == null || task.ext.when | |
| 21 | |
| 22 script: | |
| 23 def args = task.ext.args ?: '' | |
| 24 def prefix = task.index ?: '' | |
| 25 def output = 'accs_passed.txt' | |
| 26 | |
| 27 """ | |
| 28 qual_confirm.py \\ | |
| 29 -f1 $acc_passed_tool1 \\ | |
| 30 -f2 $acc_passed_tool2 | |
| 31 | |
| 32 cat <<-END_VERSIONS >> versions.yml | |
| 33 python: \$( python --version | sed 's/Python //g' ) | |
| 34 END_VERSIONS | |
| 35 """ | |
| 36 } |